Evolutionary Genomics of a Subdivided Species.
Evolutionary Genomics of a Subdivided Species.
复制标题
一个细分物种的进化基因组学。
DOI：
10.1093/molbev/msac152
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发表时间：
2022-08-03
影响因子：
10.7
通讯作者：
Lynch, Michael
中科院分区：
文献类型：
--
作者：
Maruki, Takahiro;Ye, Zhiqiang;Lynch, Michael
关键词：
遗传变异在种群内部和种群之间分布的方式是决定一个物种进化特征的关键因素。然而，对这些特征的大多数综合研究都局限于已知由局部适应驱动的环境中的细分研究，这使得我们对等位基因变异的自然分散的理解不太理想。本文对淡水微甲壳类动物水蚤（Daphnia pulex）的10个种群进行了地理种群基因组分析，水蚤是进化基因组学中一个新兴的模型系统。这些种群表现出适度的距离隔离模式，平均迁移率为每代0.6个个体，平均有效种群规模为~ 650,000个个体。大多数种群都含有大量的私有等位基因，基因组扫描突出了更多常见等位基因的过高种群细分岛屿的存在。很大一部分这样的人口分化岛可能反映了历史上的中性变化，包括罕见的随机迁移和杂交事件。尽管本研究涉及的样本量非常大，但相关变异的确切性质是分散的，不能与特定的基因座相关联，但数据确实指向了局部适应性分化。相比之下，对物种间差异的分析强调，积极选择作用于大量基因，这些基因的功能与参与局部适应的基因几乎不重叠，特别是核糖体结构、线粒体生物能量学、光接受和反应、解毒和基因调控。这些结果为利用毛霉作为模型来理解自然环境下分子和细胞进化之间的关系奠定了基础。
The ways in which genetic variation is distributed within and among populations is a key determinant of the evolutionary features of a species. However, most comprehensive studies of these features have been restricted to studies of subdivision in settings known to have been driven by local adaptation, leaving our understanding of the natural dispersion of allelic variation less than ideal. Here, we present a geographic population-genomic analysis of 10 populations of the freshwater microcrustacean Daphnia pulex, an emerging model system in evolutionary genomics. These populations exhibit a pattern of moderate isolation-by-distance, with an average migration rate of 0.6 individuals per generation, and average effective population sizes of ∼650,000 individuals. Most populations contain numerous private alleles, and genomic scans highlight the presence of islands of excessively high population subdivision for more common alleles. A large fraction of such islands of population divergence likely reflect historical neutral changes, including rare stochastic migration and hybridization events. The data do point to local adaptive divergence, although the precise nature of the relevant variation is diffuse and cannot be associated with particular loci, despite the very large sample sizes involved in this study. In contrast, an analysis of between-species divergence highlights positive selection operating on a large set of genes with functions nearly nonoverlapping with those involved in local adaptation, in particular ribosome structure, mitochondrial bioenergetics, light reception and response, detoxification, and gene regulation. These results set the stage for using D. pulex as a model for understanding the relationship between molecular and cellular evolution in the context of natural environments.
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影响因子：
3.3
作者：
Alcala, Nicolas;Rosenberg, Noah A.
通讯作者：
Rosenberg, Noah A.
影响因子：
3.3
作者：
Ackerman, Matthew S.;Johri, Parul;Lynch, Michael
通讯作者：
Lynch, Michael
DOI：
10.1073/pnas.81.19.6073
发表时间：
1984-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
CROW, JF;AOKI, K
通讯作者：
AOKI, K
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
影响因子：
1.5
作者：
Charlesworth, B;Nordborg, M;Charlesworth, D
通讯作者：
Charlesworth, D